RetrogeneDB ID: retro_mmus_648

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:61510203..61510604(-)
• Located in intron of: ENSMUSG00000037151

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Ostc
• Ensembl ID: ENSMUSG00000041084
• Aliases: Ostc, 2310008M10Rik, 5730557H03Rik
• Description: oligosaccharyltransferase complex subunit [Source:MGI Symbol;Acc:MGI:1913607]

Sequence

>retro_mmus_648
CTGGGGCTGAAGAAACTGTCCTGGGTACACATTGCCATCAGCTATGACGGTGTACACCATGGTGGTGGTATCTTACTTCC
TCATGACTGGAGGAATGATCTATGGTGTTATCGTTGAACCTCCAAGTGTTGGCTCGATGATGGATAAACATGGGCATCAG
AGACCAGTAGCTTTCTTGGCTTACAGAGTAAACGGACAGTATGTTATGGAAGGACTTGCGTCTAGCTTTCTGTTTCCAAT
GGGAGGTTTAGGTTTCATAATCCTGGACTGATCCAACACACCAAATATATCGAAACTCGACAGGTTTCTTCTTCTGTTTG
TTGGCTTTCATCTGGGTTCTACGGAGTTTCTTCATGGCTAGAGTATTCATGAGAATGAAACTGCTGGGCTACCTGATGGG
C

Alignment

ORF - retro_mmus_648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.22 %
• Parental protein coverage: 89.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKLKKPPWVH-MPSAMTVYALVVVSYFLITGGIIYDVIVEPPSVGSMTDEHGHQRPVAFLAYRVNGQYIM
          L.LKK..WVH..PSAMTVY..VVVSYFL.TGG.IY.VIVEPPSVGSM.D.HGHQRPVAFLAYRVNGQY.M
Retrocopy LGLKKLSWVH>LPSAMTVYTMVVVSYFLMTGGMIYGVIVEPPSVGSMMDKHGHQRPVAFLAYRVNGQYVM

Parental  EGLASSFLFTMGGLGFIILDRSNAPNIPKLNRFLLLFIG-FVCVLLSFFMARVFMRMKLPGYLMG
          EGLASSFLF.MGGLGFIILD.SN.PNI.KL.RFLLLF.G.F..VL.SFFMARVFMRMKL.GYLMG
Retrocopy EGLASSFLFPMGGLGFIILD*SNTPNISKLDRFLLLFVG>FIWVLRSFFMARVFMRMKLLGYLMG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.07 RPM	23.50 RPM
SRP007412_cerebellum	0.00 RPM	17.54 RPM
SRP007412_heart	0.00 RPM	19.61 RPM
SRP007412_kidney	0.04 RPM	23.12 RPM
SRP007412_liver	0.00 RPM	32.82 RPM
SRP007412_testis	0.05 RPM	11.39 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_648 was not detected

EST

No EST(s) were mapped for retro_mmus_648 retrocopy.

TSS

No TSS is located nearby retro_mmus_648 retrocopy 5' end.

Lab

retro_mmus_648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_648 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001753	2 retrocopies	retro_amel_1110, retro_amel_165,
Canis familiaris	ENSCAFG00000011286	12 retrocopies	retro_cfam_1129, retro_cfam_1206, retro_cfam_1459, retro_cfam_1462, retro_cfam_1575, retro_cfam_1851, retro_cfam_1910, retro_cfam_1948, retro_cfam_2003, retro_cfam_263, retro_cfam_296, retro_cfam_814,
Callithrix jacchus	ENSCJAG00000016002	3 retrocopies	retro_cjac_121, retro_cjac_2981, retro_cjac_324,
Cavia porcellus	ENSCPOG00000024467	1 retrocopy	retro_cpor_659,
Echinops telfairi	ENSETEG00000003717	4 retrocopies	retro_etel_1564, retro_etel_492, retro_etel_878, retro_etel_970,
Gorilla gorilla	ENSGGOG00000026873	6 retrocopies	retro_ggor_1457, retro_ggor_2060, retro_ggor_215, retro_ggor_2427, retro_ggor_370, retro_ggor_385,
Monodelphis domestica	ENSMODG00000020599	1 retrocopy	retro_mdom_428,
Mustela putorius furo	ENSMPUG00000008869	1 retrocopy	retro_mputfur_1451,
Mus musculus	ENSMUSG00000041084	1 retrocopy	retro_mmus_648 ,
Oryctolagus cuniculus	ENSOCUG00000011056	2 retrocopies	retro_ocun_1318, retro_ocun_7,
Pteropus vampyrus	ENSPVAG00000005915	1 retrocopy	retro_pvam_924,
Rattus norvegicus	ENSRNOG00000023322	1 retrocopy	retro_rnor_2297,
Sus scrofa	ENSSSCG00000009145	1 retrocopy	retro_sscr_503,
Ictidomys tridecemlineatus	ENSSTOG00000021644	6 retrocopies	retro_itri_1211, retro_itri_1386, retro_itri_15, retro_itri_1571, retro_itri_789, retro_itri_863,
Tarsius syrichta	ENSTSYG00000000724	2 retrocopies	retro_tsyr_1193, retro_tsyr_921,